io.repseq.dto

Class VDJCGeneData

java.lang.Object

io.repseq.dto.VDJCGeneData

All Implemented Interfaces:

Comparable<VDJCGeneData>

public class VDJCGeneData
extends Object
implements Comparable<VDJCGeneData>

DTO for VDJC Gene

Constructor Summary

Constructors

Constructor and Description
VDJCGeneData(BaseSequence baseSequence, String name, GeneType geneType, boolean isFunctional, Chains chains, String note, Set<GeneTag> tags, SortedMap<ReferencePoint,Long> anchorPoints)

Method Summary

Methods

Modifier and Type	Method and Description
VDJCGeneData	clone()
int	compareTo(VDJCGeneData o)
boolean	equals(Object o)
Map<ReferencePoint,Long>	getAnchorPoints()
BaseSequence	getBaseSequence()
Chains	getChains()
String	getFamilyName() Gene family name (e.g.
String	getGeneName() Name without allele index (e.g.
GeneType	getGeneType()
String	getName() Full gene name
EnumSet<GeneTag>	getTags()
int	hashCode()
boolean	isFunctional()

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VDJCGeneData

public VDJCGeneData(BaseSequence baseSequence,
            String name,
            GeneType geneType,
            boolean isFunctional,
            Chains chains,
            String note,
            Set<GeneTag> tags,
            SortedMap<ReferencePoint,Long> anchorPoints)

Method Detail

getBaseSequence

public BaseSequence getBaseSequence()

getName

public String getName()

Full gene name

Returns:

full gene name

getGeneName

public String getGeneName()

Name without allele index (e.g. TRBV12-3 for TRBV12-3*01).

Returns:

without allele index (e.g. TRBV12-3 for TRBV12-3*01)

getFamilyName

public String getFamilyName()

Gene family name (e.g. TRBV12 for TRBV12-3*01).

Returns:

gene family name (e.g. TRBV12 for TRBV12-3*01)

getGeneType

public GeneType getGeneType()

isFunctional

public boolean isFunctional()

getChains

public Chains getChains()

getTags

public EnumSet<GeneTag> getTags()

getAnchorPoints

public Map<ReferencePoint,Long> getAnchorPoints()

clone

public VDJCGeneData clone()

Overrides:

clone in class Object

compareTo

public int compareTo(VDJCGeneData o)

Specified by:

compareTo in interface Comparable<VDJCGeneData>

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object